\documentclass[$if(fontsize)$$fontsize$,$endif$$if(lang)$$babel-lang$,$endif$$if(handout)$handout,$endif$$if(beamer)$ignorenonframetext,$endif$$for(classoption)$$classoption$$sep$,$endfor$$if(make149)$,aspectratio=149$endif$]{$documentclass$}
$if(theme)$
\usetheme{$theme$}
$endif$
$if(colortheme)$
\usecolortheme{$colortheme$}
$endif$
$if(fonttheme)$
\usefonttheme{$fonttheme$}
$endif$
$if(mainfont)$
\usefonttheme{serif} % use mainfont rather than sansfont for slide text
$endif$
$if(innertheme)$
\useinnertheme{$innertheme$}
$endif$
$if(outertheme)$
\useoutertheme{$outertheme$}
$endif$
\setbeamertemplate{caption}[numbered]
\setbeamertemplate{caption label separator}{: }
\setbeamercolor{caption name}{fg=normal text.fg}
$if(fontfamily)$
\usepackage[$fontfamilyoptions$]{$fontfamily$}
$else$
\usepackage{lmodern}
$endif$
\usepackage{amssymb,amsmath}
\usepackage{ifxetex,ifluatex}
\usepackage{fixltx2e} % provides \textsubscript
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
  \usepackage[$if(fontenc)$$fontenc$$else$T1$endif$]{fontenc}
  \usepackage[utf8]{inputenc}
$if(euro)$
  \usepackage{eurosym}
$endif$
\else % if luatex or xelatex
  \ifxetex
    \usepackage{mathspec}
  \else
    \usepackage{fontspec}
  \fi
  \defaultfontfeatures{Ligatures=TeX,Scale=MatchLowercase}
  \newcommand{\euro}{€}
$if(mainfont)$
    \setmainfont[$mainfontoptions$]{$mainfont$}
$endif$
$if(sansfont)$
    \setsansfont[$sansfontoptions$]{$sansfont$}
$endif$
$if(monofont)$
    \setmonofont[Mapping=tex-ansi$if(monofontoptions)$,$monofontoptions$$endif$]{$monofont$}
$endif$
$if(mathfont)$
    \setmathfont(Digits,Latin,Greek)[$mathfontoptions$]{$mathfont$}
$endif$
$if(CJKmainfont)$
    \usepackage{xeCJK}
    \setCJKmainfont[$CJKoptions$]{$CJKmainfont$}
$endif$
\fi
% use upquote if available, for straight quotes in verbatim environments
\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
% use microtype if available
\IfFileExists{microtype.sty}{%
\usepackage{microtype}
\UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
}{}
$if(lang)$
\ifxetex
  \usepackage{polyglossia}
  \setmainlanguage[$polyglossia-lang.options$]{$polyglossia-lang.name$}
$for(polyglossia-otherlangs)$
  \setotherlanguage[$polyglossia-otherlangs.options$]{$polyglossia-otherlangs.name$}
$endfor$
\else
  \usepackage[shorthands=off,$babel-lang$]{babel}
\fi
$endif$
$if(natbib)$
\usepackage{natbib}
\bibliographystyle{$if(biblio-style)$$biblio-style$$else$plainnat$endif$}
$endif$
$if(biblatex)$
\usepackage{biblatex}
$for(bibliography)$
\addbibresource{$bibliography$}
$endfor$
$endif$
$if(listings)$
\usepackage{listings}
$endif$
$if(lhs)$
\lstnewenvironment{code}{\lstset{language=Haskell,basicstyle=\small\ttfamily}}{}
$endif$
$if(highlighting-macros)$
$highlighting-macros$
$endif$
$if(verbatim-in-note)$
\usepackage{fancyvrb}
\VerbatimFootnotes % allows verbatim text in footnotes
$endif$
$if(tables)$
\usepackage{longtable,booktabs}
\usepackage{caption}
% These lines are needed to make table captions work with longtable:
\makeatletter
\def\fnum@table{\tablename~\thetable}
\makeatother
$endif$
$if(graphics)$
\usepackage{graphicx,grffile}
\makeatletter
\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
\def\maxheight{\ifdim\Gin@nat@height>\textheight0.8\textheight\else\Gin@nat@height\fi}
\makeatother
% Scale images if necessary, so that they will not overflow the page
% margins by default, and it is still possible to overwrite the defaults
% using explicit options in \includegraphics[width, height, ...]{}
\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
$endif$

% Comment these out if you don't want a slide with just the
% part/section/subsection/subsubsection title:
\AtBeginPart{
  \let\insertpartnumber\relax
  \let\partname\relax
  \frame{\partpage}
}
\AtBeginSection{
  \let\insertsectionnumber\relax
  \let\sectionname\relax
  \frame{\sectionpage}
}
\AtBeginSubsection{
  \let\insertsubsectionnumber\relax
  \let\subsectionname\relax
  \frame{\subsectionpage}
}

$if(links-as-notes)$
% Make links footnotes instead of hotlinks:
\renewcommand{\href}[2]{#2\footnote{\url{#1}}}
$endif$
$if(strikeout)$
\usepackage[normalem]{ulem}
% avoid problems with \sout in headers with hyperref:
\pdfstringdefDisableCommands{\renewcommand{\sout}{}}
$endif$
\setlength{\emergencystretch}{3em}  % prevent overfull lines
\providecommand{\tightlist}{%
  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
$if(numbersections)$
\setcounter{secnumdepth}{5}
$else$
\setcounter{secnumdepth}{0}
$endif$
$if(dir)$
\ifxetex
  % load bidi as late as possible as it modifies e.g. graphicx
  $if(latex-dir-rtl)$
  \usepackage[RTLdocument]{bidi}
  $else$
  \usepackage{bidi}
  $endif$
\fi
\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
  \TeXXeTstate=1
  \newcommand{\RL}[1]{\beginR #1\endR}
  \newcommand{\LR}[1]{\beginL #1\endL}
  \newenvironment{RTL}{\beginR}{\endR}
  \newenvironment{LTR}{\beginL}{\endL}
\fi
$endif$

$if(title)$
\title{$title$}
$endif$
$if(subtitle)$
\subtitle{$subtitle$}
$endif$
$if(author)$
\author{$for(author)$$author$$sep$ \and $endfor$}
$endif$
\date{$date$}
$for(header-includes)$
$header-includes$
$endfor$

%% Here's everything I added.
%%--------------------------

\usepackage{graphicx}
\usepackage{rotating}
%\setbeamertemplate{caption}[numbered]
\usepackage{hyperref}
\usepackage{caption}
\usepackage[normalem]{ulem}
%\mode<presentation>
\usepackage{wasysym}
%\usepackage{amsmath}


% Get rid of navigation symbols.
%-------------------------------
\setbeamertemplate{navigation symbols}{}

% Optional institute tags and titlegraphic.
% Do feel free to change the titlegraphic if you don't want it as a Markdown field.
%----------------------------------------------------------------------------------
$if(institute)$\institute{$institute$}$endif$

% \titlegraphic{\includegraphics[width=0.3\paperwidth]{\string~/Dropbox/teaching/clemson-academic.png}} % <-- if you want to know what this looks like without it as a Markdown field. 
% -----------------------------------------------------------------------------------------------------
$if(titlegraphic)$\titlegraphic{\includegraphics[width=0.3\paperwidth]{\string~$titlegraphic$}}$endif$

% Some additional title page adjustments.
%----------------------------------------
\setbeamertemplate{title page}[empty]
%\date{}
\setbeamerfont{subtitle}{size=\small}

\setbeamercovered{transparent}

% Some optional colors. Change or add as you see fit.
%---------------------------------------------------
\definecolor{clemsonpurple}{HTML}{522D80}
 \definecolor{clemsonorange}{HTML}{F66733}
\definecolor{uiucblue}{HTML}{003C7D}
\definecolor{uiucorange}{HTML}{F47F24}


% Some optional color adjustments to Beamer. Change as you see fit.
%------------------------------------------------------------------
\setbeamercolor{frametitle}{fg=clemsonpurple,bg=white}
\setbeamercolor{title}{fg=clemsonpurple,bg=white}
\setbeamercolor{local structure}{fg=clemsonpurple}
\setbeamercolor{section in toc}{fg=clemsonpurple,bg=white}
% \setbeamercolor{subsection in toc}{fg=clemsonorange,bg=white}
\setbeamercolor{footline}{fg=clemsonpurple!50, bg=white}
\setbeamercolor{block title}{fg=clemsonorange,bg=white}


\let\Tiny=\tiny


% Sections and subsections should not get their own damn slide.
%--------------------------------------------------------------
\AtBeginPart{}
\AtBeginSection{}
\AtBeginSubsection{}
\AtBeginSubsubsection{}

% Suppress some of Markdown's weird default vertical spacing.
%------------------------------------------------------------
\setlength{\emergencystretch}{0em}  % prevent overfull lines
\setlength{\parskip}{0pt}


% Allow for those simple two-tone footlines I like. 
% Edit the colors as you see fit.
%--------------------------------------------------
\defbeamertemplate*{footline}{my footline}{%
    \ifnum\insertpagenumber=1
    \hbox{%
        \begin{beamercolorbox}[wd=\paperwidth,ht=.8ex,dp=1ex,center]{}%
      % empty environment to raise height
        \end{beamercolorbox}%
    }%
    \vskip0pt%
    \else%
        \Tiny{%
            \hfill%
		\vspace*{1pt}%
            \insertframenumber/\inserttotalframenumber \hspace*{0.1cm}%
            \newline%
            \color{clemsonpurple}{\rule{\paperwidth}{0.4mm}}\newline%
            \color{clemsonorange}{\rule{\paperwidth}{.4mm}}%
        }%
    \fi%
}

% Various cosmetic things, though I must confess I forget what exactly these do and why I included them.
%-------------------------------------------------------------------------------------------------------
\setbeamercolor{structure}{fg=blue}
\setbeamercolor{local structure}{parent=structure}
\setbeamercolor{item projected}{parent=item,use=item,fg=clemsonpurple,bg=white}
\setbeamercolor{enumerate item}{parent=item}

% Adjust some item elements. More cosmetic things.
%-------------------------------------------------
\setbeamertemplate{itemize item}{\color{clemsonpurple}$$\bullet$$}
\setbeamertemplate{itemize subitem}{\color{clemsonpurple}\scriptsize{$$\bullet$$}}
\setbeamertemplate{itemize/enumerate body end}{\vspace{.6\baselineskip}} % So I'm less inclined to use \medskip and \bigskip in Markdown.

% Automatically center images
% ---------------------------
% Note: this is for ![](image.png) images
% Use "fig.align = "center" for R chunks

\usepackage{etoolbox}

\AtBeginDocument{%
  \letcs\oig{@orig\string\includegraphics}%
  \renewcommand<>\includegraphics[2][]{%
    \only#3{%
      {\centering\oig[{#1}]{#2}\par}%
    }%
  }%
}

% I think I've moved to xelatex now. Here's some stuff for that.
% --------------------------------------------------------------
% I could customize/generalize this more but the truth is it works for my circumstances.

\ifxetex
\setbeamerfont{title}{family=\fontspec{$if(titlefont)$$titlefont$$else$serif$endif$}}
\setbeamerfont{frametitle}{family=\fontspec{$if(titlefont)$$titlefont$$else$serif$endif$}}
\usepackage[font=small,skip=0pt]{caption}
 \else
 \fi

% Okay, and begin the actual document...

\begin{document}
$if(title)$
\frame{\titlepage}
$endif$

$for(include-before)$
$include-before$

$endfor$
$if(toc)$
\begin{frame}
\tableofcontents[hideallsubsections]
\end{frame}

$endif$
$body$

$if(natbib)$
$if(bibliography)$
$if(biblio-title)$
$if(book-class)$
\renewcommand\bibname{$biblio-title$}
$else$
\renewcommand\refname{$biblio-title$}
$endif$
$endif$
\begin{frame}[allowframebreaks]{$biblio-title$}
\bibliography{$for(bibliography)$$bibliography$$sep$,$endfor$}
\end{frame}

$endif$
$endif$
$if(biblatex)$
\begin{frame}[allowframebreaks]{$biblio-title$}
\printbibliography[heading=none]
\end{frame}

$endif$
$for(include-after)$
$include-after$

$endfor$

\section[]{}
\frame{\small \frametitle{Table of Contents}
\tableofcontents}
\end{document}
